A provenance change driven by tectonic and climatic forcing records the surface geodynamic processes, and is of great significance for our understanding of evolving continental margins. The Paleogene succession in the Pearl River Mouth Basin (PRMB), northern South China Sea (SCS), records the variation of sediment-routing systems and thus can reveal provenance changes and their association with the regional paleogeographic evolution on the South China margin. We use U–Pb ages and the Eu/Eu* anomalies of detrital zircons from Paleogene samples in Huizhou Sag, northern PRMB to reconstruct the sediment-routing system and the crustal thickness of the South China margin, respectively. The results show that from the middle Eocene to the upper Eocene there was a rapid increase in proportion of old-age zircon populations (>200 Ma), reflecting a provenance change from the intrabasinal Mesozoic basement to the extrabasinal South China Block. Moreover, the Eu/Eu* anomalies in detrital zircons suggest that during Cretaceous the crustal thickness increased from ca. 40 km to ca. 70 km in the South China margin, corresponding to the uplift of the extensive Coastal Mountains along the South China margin. The substantial rock uplift is believed to be related to the subduction between the Cretaceous Izanagi Plate and the South China Block. A new paleogeographic pattern is reconstructed, where we relate the late Eocene provenance change to the relief generated by the Cretaceous orogenic event. Firstly, due to the rain shadow effect, the uplift of the Coastal Mountains prevented pacific air from reaching into the South China hinterland, causing the northwestern side of the Coastal Mountains to be arid whereas the southeastern side being humid. Then, on the humid southeastern foothills, the paleo-Pearl River originated from the Late Cretaceous to the middle Eocene and transported more and more sediments from the South China Block to PRMB since the late Eocene, causing the provenance change from the intrabasinal basement to extrabasinal South China Block.